deltaCaptureC
Bioc currentThis Package Discovers Meso-scale Chromatin Remodeling from 3C Data
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred 'viewpoint' region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
19 17 exported
Complexity
2.7 avg / 7 max
Call network
19 nodes / 18 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
1,914
Files
69
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
2
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2019-10-29
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 41
- Examples that run
- 100%14 run in a plain check
- Exported functions with examples
- 82%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Delta Capture-C HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| bigBinSize | vector | 1 element | 3 packages |
| binnedDeltaPlot | gg | 11 elements | No other package |
| binnedDeltaSE | – | – | – |
| binnedSummarizedExperiment | – | – | – |
| deltaSE | – | – | – |
| miniDeltaSE | – | – | – |
| miniSE | – | – | – |
| miniSEDF | data.frame | 1,909 × 7 | No other package |
| numPermutations | vector | 1 element | 5 packages |
| pValue | vector | 1 element | 4 packages |
| plotTitle | vector | 1 element | No other package |
| regionOfInterest | – | – | – |
| significanceType | vector | 1 element | No other package |
| significantRegions | – | – | – |
| significantRegionsPlot | gg | 11 elements | No other package |
| smallBinSize | vector | 1 element | 5 packages |
| smallBins | – | – | – |
| smallSetOfSmallBins | – | – | – |
| smallerDeltaSE | – | – | – |
| viewpointRegion | – | – | – |
| weightsExampleBins | – | – | – |
| weightsExampleGr | – | – | – |
Topics
People
- Michael Shapiro author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("deltaCaptureC")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.